Pub Date : 2024-09-14DOI: 10.1007/s00294-024-01301-w
Sara Mina, Anaïs Hérivaux, Hajar Yaakoub, Vincent Courdavault, Méline Wéry, Nicolas Papon
Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.
双组分系统(TCS)是一种多样化的细胞信号传导途径,在原核生物和真核生物应对各种环境信号时发挥着重要作用。这些转导回路主要由组氨酸激酶(HKs)控制,它们是各种压力源的传感蛋白。迄今为止,真菌王国已描述了 19 个 HK 组。然而,迄今为止,我们只在有限的真菌物种中研究了这些突出的传感蛋白的结构和分布。在本研究中,我们利用最近的真菌基因组资源,通过破译大量真菌支系中 HKs 的结构多样性和系统发育分布,完善了真菌 HK 的分类。为此,我们浏览了不同真菌支系中具有代表性的 91 个物种的基因组,得到了 726 个预测的 HK 序列。通过域组织分析和稳健的系统发生学方法,我们改进了真菌 HKs 的分类。虽然大部分编译序列被归入了之前描述的真菌 HK 群组,但也定义了一些新的群组。总之,这项研究改进了真菌王国中 HKs 的结构、分布和进化概况。
{"title":"Structure and distribution of sensor histidine kinases in the fungal kingdom","authors":"Sara Mina, Anaïs Hérivaux, Hajar Yaakoub, Vincent Courdavault, Méline Wéry, Nicolas Papon","doi":"10.1007/s00294-024-01301-w","DOIUrl":"https://doi.org/10.1007/s00294-024-01301-w","url":null,"abstract":"<p>Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Histidine kinases (HKs) are important sensor proteins in fungi and play an essential role in environmental adaptation. However, the mechanisms by which fungi sense and respond to fungivores attack via HKs are not fully understood. In this study, we utilized Neurospora crassa to investigate the involvement of HKs in responding to fungivores attack. We found that the 11 HKs in N. crassa not only affected the growth and development, but also led to fluctuations in antioxidant production. Ten mutants in the genes encoding HKs (except ∆phy1) showed increased production of reactive oxygen species (ROS), especially upon Sinella curviseta attack. The ROS burst triggered changes in conidia and perithecial beaks formation, as well as accumulation of β-glucan, ergothioneine, ergosterol, and carotenoids. β-glucan was increased in ∆hk9, ∆os1, ∆hcp1, ∆nik2, ∆sln1, ∆phy1 and ∆phy2 mutants compared to the wild-type strain. In parallel, ergothioneine accumulation was improved in ∆phy1 and ∆hk16 mutants and further increased upon attack, except in ∆os1 and ∆hk16 mutants. Additionally, fungivores attack stimulated ergosterol and dehydroergosterol production in ∆hk9 and ∆os1 mutants. Furthermore, deletion of these genes altered carotenoid accumulation, with wild-type strain, ∆hk9, ∆os1, ∆hcp1, ∆sln1, ∆phy2, and ∆dcc1mutants showing an increase in carotenoids upon attack. Taken together, HKs are involved in regulating the production of conidia and antioxidants. Thus, HKs may act as sensors of fungivores attack and effectively improve the adaptive capacity of fungi to environmental stimuli.
{"title":"Adaptative responses of Neurospora crassa by histidine kinases upon the attack of the arthropod Sinella curviseta","authors":"Ting Lu, Xiao-meng Wang, Peng-xu Chen, Juan Xi, Han-bing Yang, Wei-fa Zheng, Yan-xia Zhao","doi":"10.1007/s00294-024-01302-9","DOIUrl":"https://doi.org/10.1007/s00294-024-01302-9","url":null,"abstract":"<p>Histidine kinases (HKs) are important sensor proteins in fungi and play an essential role in environmental adaptation. However, the mechanisms by which fungi sense and respond to fungivores attack via HKs are not fully understood. In this study, we utilized <i>Neurospora crassa</i> to investigate the involvement of HKs in responding to fungivores attack. We found that the 11 HKs in <i>N. crassa</i> not only affected the growth and development, but also led to fluctuations in antioxidant production. Ten mutants in the genes encoding HKs (except ∆<i>phy1</i>) showed increased production of reactive oxygen species (ROS), especially upon <i>Sinella curviseta</i> attack. The ROS burst triggered changes in conidia and perithecial beaks formation, as well as accumulation of β-glucan, ergothioneine, ergosterol, and carotenoids. β-glucan was increased in ∆<i>hk9</i>, ∆<i>os1</i>, ∆<i>hcp1</i>, ∆<i>nik2</i>, ∆<i>sln1</i>, ∆<i>phy1</i> and ∆<i>phy2</i> mutants compared to the wild-type strain. In parallel, ergothioneine accumulation was improved in ∆<i>phy1</i> and ∆<i>hk16</i> mutants and further increased upon attack, except in ∆<i>os1</i> and ∆<i>hk16</i> mutants. Additionally, fungivores attack stimulated ergosterol and dehydroergosterol production in ∆<i>hk9</i> and ∆<i>os1</i> mutants. Furthermore, deletion of these genes altered carotenoid accumulation, with wild-type strain, ∆<i>hk9</i>, ∆<i>os1</i>, ∆<i>hcp1</i>, ∆<i>sln1</i>, ∆<i>phy2</i>, and ∆<i>dcc1</i>mutants showing an increase in carotenoids upon attack. Taken together, HKs are involved in regulating the production of conidia and antioxidants. Thus, HKs may act as sensors of fungivores attack and effectively improve the adaptive capacity of fungi to environmental stimuli.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromatin remodelling complexes (CRC) are ATP-dependent molecular machines important for the dynamic organization of nucleosomes along eukaryotic DNA. CRCs SWI/SNF, RSC and INO80 can move positioned nucleosomes in promoter DNA, leading to nucleosome-depleted regions which facilitate access of general transcription factors. This function is strongly supported by transcriptional activators being able to interact with subunits of various CRCs. In this work we show that SWI/SNF subunits Swi1, Swi2, Snf5 and Snf6 can bind to activation domains of Ino2 required for expression of phospholipid biosynthetic genes in yeast. We identify an activator binding domain (ABD) of ATPase Swi2 and show that this ABD is functionally dispensable, presumably because ABDs of other SWI/SNF subunits can compensate for the loss. In contrast, mutational characterization of the ABD of the Swi2-related ATPase Sth1 revealed that some conserved basic and hydrophobic amino acids within this domain are essential for the function of Sth1. While ABDs of Swi2 and Sth1 define separate functional protein domains, mapping of an ABD within ATPase Ino80 showed co-localization with its HSA domain also required for binding actin-related proteins. Comparative interaction studies finally demonstrated that several unrelated activators each exhibit a specific binding pattern with ABDs of Swi2, Sth1 and Ino80.
染色质重塑复合体(CRC)是一种依赖于 ATP 的分子机器,对于核小体沿真核 DNA 的动态组织非常重要。染色质重塑复合体 SWI/SNF、RSC 和 INO80 可移动启动子 DNA 中定位的核小体,从而形成核小体缺失区,有利于一般转录因子的进入。转录激活因子能与各种 CRCs 的亚基相互作用,从而有力地支持了这一功能。在这项工作中,我们发现 SWI/SNF 亚基 Swi1、Swi2、Snf5 和 Snf6 能与酵母中磷脂生物合成基因表达所需的 Ino2 激活结构域结合。我们确定了 ATPase Swi2 的激活剂结合结构域(ABD),并证明该 ABD 在功能上是可有可无的,这可能是因为其他 SWI/SNF 亚基的 ABD 可以弥补该 ABD 的缺失。与此相反,对 Swi2 相关 ATPase Sth1 的 ABD 进行突变表征后发现,该结构域中一些保守的碱性和疏水氨基酸对 Sth1 的功能至关重要。虽然 Swi2 和 Sth1 的 ABD 定义了不同的蛋白质功能域,但 ATPase Ino80 内 ABD 的图谱显示,该 ABD 与其 HSA 结构域共定位,后者也是结合肌动蛋白相关蛋白所必需的。相互作用比较研究最终表明,几种不相关的激活剂都表现出与 Swi2、Sth1 和 Ino80 的 ABD 的特定结合模式。
{"title":"Transcriptional activation domains interact with ATPase subunits of yeast chromatin remodelling complexes SWI/SNF, RSC and INO80.","authors":"Eva-Carina Wendegatz, Maike Engelhardt, Hans-Joachim Schüller","doi":"10.1007/s00294-024-01300-x","DOIUrl":"10.1007/s00294-024-01300-x","url":null,"abstract":"<p><p>Chromatin remodelling complexes (CRC) are ATP-dependent molecular machines important for the dynamic organization of nucleosomes along eukaryotic DNA. CRCs SWI/SNF, RSC and INO80 can move positioned nucleosomes in promoter DNA, leading to nucleosome-depleted regions which facilitate access of general transcription factors. This function is strongly supported by transcriptional activators being able to interact with subunits of various CRCs. In this work we show that SWI/SNF subunits Swi1, Swi2, Snf5 and Snf6 can bind to activation domains of Ino2 required for expression of phospholipid biosynthetic genes in yeast. We identify an activator binding domain (ABD) of ATPase Swi2 and show that this ABD is functionally dispensable, presumably because ABDs of other SWI/SNF subunits can compensate for the loss. In contrast, mutational characterization of the ABD of the Swi2-related ATPase Sth1 revealed that some conserved basic and hydrophobic amino acids within this domain are essential for the function of Sth1. While ABDs of Swi2 and Sth1 define separate functional protein domains, mapping of an ABD within ATPase Ino80 showed co-localization with its HSA domain also required for binding actin-related proteins. Comparative interaction studies finally demonstrated that several unrelated activators each exhibit a specific binding pattern with ABDs of Swi2, Sth1 and Ino80.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-16DOI: 10.1007/s00294-024-01299-1
Mauro M S Saraiva, Valdinete P Benevides, Priscila R Guerra, Isabella C Campos, Lucas B Rodrigues Alves, Jacqueline B Paiva, Lauanda M Muniz, Adriana M Almeida, Oliveiro C Freitas Neto, John E Olsen, Angelo Berchieri Junior
In mammals, enteric salmonellas can use tetrathionate (ttr), formed as a by-product from the inflammatory process in the intestine, as electron acceptor in anaerobic respiration, and it can fuel its energy metabolism by degrading the microbial fermentation product 1,2-propanediol. However, recent studies have shown that this mechanism is not important for Salmonella infection in the intestine of poultry, while it prolongs the persistence of Salmonella at systemic sites in this species. In the current study, we show that ΔttrApduA strains of Salmonella enterica have lower net survival within chicken-derived HD-11 macrophages, as CFU was only 2.3% (S. Enteritidis ΔttrApduA), 2.3% (S. Heidelberg ΔttrApduA), and 3.0% (S. Typhimurium ΔttrApduA) compared to wild-type strains after 24 h inside HD-11 macrophage cells. The difference was not related to increased lysis of macrophages, and deletion of ttrA and pduA did not impair the ability of the strains to grow anaerobically. Further studies are indicated to determine the reason why Salmonella ΔttrApduA strains survive less well inside macrophage cell lines.
{"title":"Deletions of ttrA and pduA genes in Salmonella enterica affect survival within chicken-derived HD-11 macrophages.","authors":"Mauro M S Saraiva, Valdinete P Benevides, Priscila R Guerra, Isabella C Campos, Lucas B Rodrigues Alves, Jacqueline B Paiva, Lauanda M Muniz, Adriana M Almeida, Oliveiro C Freitas Neto, John E Olsen, Angelo Berchieri Junior","doi":"10.1007/s00294-024-01299-1","DOIUrl":"10.1007/s00294-024-01299-1","url":null,"abstract":"<p><p>In mammals, enteric salmonellas can use tetrathionate (ttr), formed as a by-product from the inflammatory process in the intestine, as electron acceptor in anaerobic respiration, and it can fuel its energy metabolism by degrading the microbial fermentation product 1,2-propanediol. However, recent studies have shown that this mechanism is not important for Salmonella infection in the intestine of poultry, while it prolongs the persistence of Salmonella at systemic sites in this species. In the current study, we show that ΔttrApduA strains of Salmonella enterica have lower net survival within chicken-derived HD-11 macrophages, as CFU was only 2.3% (S. Enteritidis ΔttrApduA), 2.3% (S. Heidelberg ΔttrApduA), and 3.0% (S. Typhimurium ΔttrApduA) compared to wild-type strains after 24 h inside HD-11 macrophage cells. The difference was not related to increased lysis of macrophages, and deletion of ttrA and pduA did not impair the ability of the strains to grow anaerobically. Further studies are indicated to determine the reason why Salmonella ΔttrApduA strains survive less well inside macrophage cell lines.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1007/s00294-024-01298-2
Nekkanti Aarthi, Vinod K Dubey, Arakalagud N Shylesha, Aditya Kukreti, Jagadeesh Patil, Keerthi M Chandrashekara, Kandan Aravindaram, Ruqiya Seegenahalli, Nanditha Shivakumar, Manjunatha Channappa
Bacillus thuringiensis is the most widely used biopesticide, targets a diversity of insect pests belonging to several orders. However, information regarding the B. thuringiensis strains and toxins targeting Zeugodacus cucurbitae is very limited. Therefore, in the present study, we isolated and identified five indigenous B. thuringiensisstrains toxic to larvae of Z. cucurbitae. However, of five strains NBAIR BtPl displayed the highest mortality (LC50 = 37.3 μg/mL) than reference strain B. thuringiensis var. israelensis (4Q1) (LC50 = 45.41 μg/mL). Therefore, the NBAIR BtPl was considered for whole genome sequencing to identify the cry genes present in it. Whole genome sequencing of our strain revealed genome size of 6.87 Mb with 34.95% GC content. Homology search through the BLAST algorithm revealed that NBAIR BtPl is 99.8% similar to B. thuringiensis serovar tolworthi, and gene prediction through Prokka revealed 7406 genes, 7168 proteins, 5 rRNAs, and 66 tRNAs. BtToxin_Digger analysis of NBAIR BtPl genome revealed four cry gene families: cry1, cry2, cry8Aa1, and cry70Aa1. When tested for the presence of these four cry genes in other indigenous strains, results showed that cry70Aa1 was absent. Thus, the study provided a basis for predicting cry70Aa1 be the possible reason for toxicity. In this study apart from novel genes, we also identified other virulent genes encoding zwittermicin, chitinase, fengycin, and bacillibactin. Thus, the current study aids in predicting potential toxin-encoding genes responsible for toxicity to Z. cucurbitae and thus paves the way for the development of B. thuringiensis-based formulations and transgenic crops for management of dipteran pests.
{"title":"Insights into the whole genome sequence of Bacillus thuringiensis NBAIR BtPl, a strain toxic to the melon fruit fly, Zeugodacus cucurbitae.","authors":"Nekkanti Aarthi, Vinod K Dubey, Arakalagud N Shylesha, Aditya Kukreti, Jagadeesh Patil, Keerthi M Chandrashekara, Kandan Aravindaram, Ruqiya Seegenahalli, Nanditha Shivakumar, Manjunatha Channappa","doi":"10.1007/s00294-024-01298-2","DOIUrl":"https://doi.org/10.1007/s00294-024-01298-2","url":null,"abstract":"<p><p>Bacillus thuringiensis is the most widely used biopesticide, targets a diversity of insect pests belonging to several orders. However, information regarding the B. thuringiensis strains and toxins targeting Zeugodacus cucurbitae is very limited. Therefore, in the present study, we isolated and identified five indigenous B. thuringiensisstrains toxic to larvae of Z. cucurbitae. However, of five strains NBAIR BtPl displayed the highest mortality (LC<sub>50</sub> = 37.3 μg/mL) than reference strain B. thuringiensis var. israelensis (4Q1) (LC<sub>50</sub> = 45.41 μg/mL). Therefore, the NBAIR BtPl was considered for whole genome sequencing to identify the cry genes present in it. Whole genome sequencing of our strain revealed genome size of 6.87 Mb with 34.95% GC content. Homology search through the BLAST algorithm revealed that NBAIR BtPl is 99.8% similar to B. thuringiensis serovar tolworthi, and gene prediction through Prokka revealed 7406 genes, 7168 proteins, 5 rRNAs, and 66 tRNAs. BtToxin_Digger analysis of NBAIR BtPl genome revealed four cry gene families: cry1, cry2, cry8Aa1, and cry70Aa1. When tested for the presence of these four cry genes in other indigenous strains, results showed that cry70Aa1 was absent. Thus, the study provided a basis for predicting cry70Aa1 be the possible reason for toxicity. In this study apart from novel genes, we also identified other virulent genes encoding zwittermicin, chitinase, fengycin, and bacillibactin. Thus, the current study aids in predicting potential toxin-encoding genes responsible for toxicity to Z. cucurbitae and thus paves the way for the development of B. thuringiensis-based formulations and transgenic crops for management of dipteran pests.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-02DOI: 10.1007/s00294-024-01296-4
María Soledad Anzuay, Mario Hernán Chiatti, Ariana Belén Intelangelo, Liliana Mercedes Ludueña, Natalia Pin Viso, Jorge Guillermo Angelini, Tania Taurian
Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.
土壤细菌对不溶性磷化合物的溶解具有重要意义,因为它能使植物利用磷。有机酸的产生是不溶性无机磷化合物溶解的主要微生物机制。在革兰氏阴性细菌中,葡萄糖酸是由名为 GDH-PQQ 的全酶葡萄糖脱氢酶-吡咯喹啉醌的活性合成的。使用标记基因是一种非常有用的工具,可以评估引入细菌的持久性,并跟踪生物和非生物因素对土壤中这些有益微生物的影响。在之前的研究中,我们在大量不可培养和可培养的本地土壤细菌中检测到了 pqqE 基因的存在。本研究的目的是分析 pqqE 基因序列的系统发育及其在研究纯细菌培养物、混合细菌培养物和根瘤土壤样本中磷酸盐溶解细菌方面的潜力。为此,通过聚合酶链式反应(PCR)测定了属于几种细菌的磷酸盐溶解细菌基因组中 pqqE 基因的存在情况。此外,还分析了与接种或未接种磷酸盐溶解细菌的花生植株相关的混合细菌培养物和根瘤土壤中的该基因。为此,使用了从多个细菌属设计的退化引物和本研究为假单胞菌属设计的特异引物。使用两种不同的 DNA 提取技术从简单或混合细菌培养物以及根瘤土壤样本中获得 DNA 模板。结果表明,在分析的所有革兰氏阴性磷酸盐溶解菌的基因组中都发现了 pqqE 基因扩增产物。在这些细菌与其他微生物共同生长的混合培养物中获得的 DNA 中,以及在接种或未接种这些细菌的根瘤土壤样本中获得的 DNA 中,都能检测到该基因。系统进化分析表明,pqqE 基因是相关属中的保守基因。总之,pqqE 基因可能是研究磷酸盐溶解细菌种群的潜在标记。
{"title":"Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants.","authors":"María Soledad Anzuay, Mario Hernán Chiatti, Ariana Belén Intelangelo, Liliana Mercedes Ludueña, Natalia Pin Viso, Jorge Guillermo Angelini, Tania Taurian","doi":"10.1007/s00294-024-01296-4","DOIUrl":"10.1007/s00294-024-01296-4","url":null,"abstract":"<p><p>Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genus Staphylococcus encompasses a diverse array of bacteria with significant implications for human health, including disreputable pathogens such as Staphylococcus aureus and Staphylococcus epidermidis. Understanding the genetic composition and codon usage patterns of Staphylococcus species is crucial for unraveling their evolutionary dynamics, adaptive strategies, and pathogenic potential. In this study, we conducted a comprehensive analysis of codon usage patterns across 48 species within the Staphylococcus genus. Our findings uncovered variations in genomic G-C content across Staphylococcus species, impacting codon usage preferences, with a notable preference for A/T-rich codons observed in pathogenic strains. This preference for A/T-rich codons suggests an energy-saving strategy in pathogenic organisms. Analysis of dinucleotide pair expression patterns unveiled insights into genomic dynamics, with overrepresented codon pairs reflecting trends in dinucleotide expression across genomes. Additionally, a significant correlation between CAI and genomic G-C content underscored the intricate relationship between codon usage patterns and gene expression strategies. Amino acid usage analysis highlighted preferences for energetically cheaper amino acids, suggesting adaptive strategies promoting energy efficiency. This comprehensive analysis sheds light on the evolutionary dynamics and adaptive mechanisms employed by Staphylococcus species, providing valuable insights into their pathogenic potential and clinical implications. Understanding these genomic features is crucial for devising strategies to combat staphylococcal infections and improve public health outcomes.
{"title":"Comparative genome wise analysis of codon usage of Staphylococcus Genus.","authors":"Pinky Arora, Chandra Shekhar Mukhopadhyay, Sandeep Kaur","doi":"10.1007/s00294-024-01297-3","DOIUrl":"https://doi.org/10.1007/s00294-024-01297-3","url":null,"abstract":"<p><p>The genus Staphylococcus encompasses a diverse array of bacteria with significant implications for human health, including disreputable pathogens such as Staphylococcus aureus and Staphylococcus epidermidis. Understanding the genetic composition and codon usage patterns of Staphylococcus species is crucial for unraveling their evolutionary dynamics, adaptive strategies, and pathogenic potential. In this study, we conducted a comprehensive analysis of codon usage patterns across 48 species within the Staphylococcus genus. Our findings uncovered variations in genomic G-C content across Staphylococcus species, impacting codon usage preferences, with a notable preference for A/T-rich codons observed in pathogenic strains. This preference for A/T-rich codons suggests an energy-saving strategy in pathogenic organisms. Analysis of dinucleotide pair expression patterns unveiled insights into genomic dynamics, with overrepresented codon pairs reflecting trends in dinucleotide expression across genomes. Additionally, a significant correlation between CAI and genomic G-C content underscored the intricate relationship between codon usage patterns and gene expression strategies. Amino acid usage analysis highlighted preferences for energetically cheaper amino acids, suggesting adaptive strategies promoting energy efficiency. This comprehensive analysis sheds light on the evolutionary dynamics and adaptive mechanisms employed by Staphylococcus species, providing valuable insights into their pathogenic potential and clinical implications. Understanding these genomic features is crucial for devising strategies to combat staphylococcal infections and improve public health outcomes.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-31DOI: 10.1007/s00294-024-01295-5
Damanjeet Kaur, Vijay Singh, Saurabh Gupta
Cloning and expression of a gene in the desired host is required for optimum production in recombinant strains. The present research is the first attempt to optimize the physiological conditions for the transformation of Pseudomonas aeruginosa SDK-6 with pJN105. Different factors, such as inoculum size, incubation period, heat shock temperature, and heat shock time were optimized using one factor at a time (OFAT) followed by the selection of transformants using gentamicin resistance marker. The maximum number of transformants (2.002 ± 0.077 × 105 cfu/ µg of plasmid DNA) were reported with 0.5% (v/v) inoculum, an incubation period of 3 h, and heat shock treatment at 50 °C for 1 min. An overall 12-fold increase in transformation efficiency was observed. The presence of a 6055 bp band on agarose gel confirmed the transformation of Pseudomonas aeruginosa with the vector pJN105.
{"title":"Optimizing CaCl<sub>2</sub>-mediated transformation of Pseudomonas aeruginosa SDK-6 with pJN105 using OFAT: A novel and efficient cloning approach.","authors":"Damanjeet Kaur, Vijay Singh, Saurabh Gupta","doi":"10.1007/s00294-024-01295-5","DOIUrl":"https://doi.org/10.1007/s00294-024-01295-5","url":null,"abstract":"<p><p>Cloning and expression of a gene in the desired host is required for optimum production in recombinant strains. The present research is the first attempt to optimize the physiological conditions for the transformation of Pseudomonas aeruginosa SDK-6 with pJN105. Different factors, such as inoculum size, incubation period, heat shock temperature, and heat shock time were optimized using one factor at a time (OFAT) followed by the selection of transformants using gentamicin resistance marker. The maximum number of transformants (2.002 ± 0.077 × 10<sup>5</sup> cfu/ µg of plasmid DNA) were reported with 0.5% (v/v) inoculum, an incubation period of 3 h, and heat shock treatment at 50 °C for 1 min. An overall 12-fold increase in transformation efficiency was observed. The presence of a 6055 bp band on agarose gel confirmed the transformation of Pseudomonas aeruginosa with the vector pJN105.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1007/s00294-024-01294-6
Mareike Rij, Jürgen Wendland
The ability to regulate the expression of genes is a central tool for the characterization of fungal genes. This is of particular interest to study genes required for specific processes or the effect of genes expressed only under specific conditions. Saccharomycopsis species show a unique property of necrotrophic mycoparasitism that is activated upon starvation. Here we describe the use of the MET17 promoter of S. schoenii as a tool to regulate gene expression based on the availability of methionine. Conditional expression was tested using lacZ and GFP reporter genes. Gene expression could be strongly down-regulated by the addition of methionine or cysteine to the growth medium and upregulated by starvation for methionine. We used X-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) to detect lacZ-expression in plate assays and ONPG (ortho-nitrophenyl-β-galactopyranoside) as a substrate for β-galactosidase in liquid-phase assays. For in vivo expression analyses we used fluorescence microscopy for the detection and localization of a MET17-driven histone H4-GFP reporter gene. With these assays we demonstrated the usefulness of the MET17 promoter to regulate expression of genes based on methionine availability. In silico analyses revealed similar promoter motifs as found in MET3 genes of Saccharomyces cerevisiae and Ashbya gossypii. This suggests a regulation of the MET17 promoter by CBF1 and MET31/MET32 in conjunction with the transcriptional activator MET4, which were also identified in the S. schoenii genome.
{"title":"Use of the Saccharomycopsis schoenii MET17 promoter for regulated heterologous gene expression.","authors":"Mareike Rij, Jürgen Wendland","doi":"10.1007/s00294-024-01294-6","DOIUrl":"10.1007/s00294-024-01294-6","url":null,"abstract":"<p><p>The ability to regulate the expression of genes is a central tool for the characterization of fungal genes. This is of particular interest to study genes required for specific processes or the effect of genes expressed only under specific conditions. Saccharomycopsis species show a unique property of necrotrophic mycoparasitism that is activated upon starvation. Here we describe the use of the MET17 promoter of S. schoenii as a tool to regulate gene expression based on the availability of methionine. Conditional expression was tested using lacZ and GFP reporter genes. Gene expression could be strongly down-regulated by the addition of methionine or cysteine to the growth medium and upregulated by starvation for methionine. We used X-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) to detect lacZ-expression in plate assays and ONPG (ortho-nitrophenyl-β-galactopyranoside) as a substrate for β-galactosidase in liquid-phase assays. For in vivo expression analyses we used fluorescence microscopy for the detection and localization of a MET17-driven histone H4-GFP reporter gene. With these assays we demonstrated the usefulness of the MET17 promoter to regulate expression of genes based on methionine availability. In silico analyses revealed similar promoter motifs as found in MET3 genes of Saccharomyces cerevisiae and Ashbya gossypii. This suggests a regulation of the MET17 promoter by CBF1 and MET31/MET32 in conjunction with the transcriptional activator MET4, which were also identified in the S. schoenii genome.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11217035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Byr2 kinase of fission yeast Schizosaccharomyces pombe is recruited to the membrane with the assistance of Ras1. Byr2 is also negatively regulated by 14-3-3 proteins encoded by rad24 and rad25. We conducted domain and mutational analysis of Byr2 to determine which region is critical for its binding to 14-3-3 proteins. Rad24 and Rad25 bound to both the Ras interaction domain in the N-terminus and to the C-terminal catalytic domain of Byr2. When amino acid residues S87 and T94 of the Ras-interacting domain of Byr2 were mutated to alanine, Rad24 could no longer bind to Byr2. S402, S566, S650, and S654 mutations in the C-terminal domain of Byr2 also abolished its interaction with Rad24 and Rad25. More than three mutations in the C-terminal domain were required to abolish completely its interaction with 14-3-3 protein, suggesting that multiple residues are involved in this interaction. Expression of the N-terminal domain of Byr2 in wild-type cells lowered the mating ratio, because it likely blocked the interaction of Byr2 with Ste4 and Ras1, whereas expression of the catalytic domain of Byr2 increased the mating ratio as a result of freeing from intramolecular regulation by the N-terminal domain of Byr2. The S87A and T94A mutations of Byr2 increased the mating ratio and attenuated inhibition of Byr2 by Rad24; therefore, these two amino acids are critical for its regulation by Rad24. S566 of Byr2 is critical for activity of Byr2 but not for its interaction with 14-3-3 proteins. In this study, we show that 14-3-3 proteins interact with two separate domains in Byr2 as negative regulators.
{"title":"Mutational analyses of the interacting domains of Schizosaccharomyces pombe Byr2 with 14-3-3s.","authors":"Yasuyo Kobayashi-Ooka, Fumiyo Ozoe, Makoto Kawamukai","doi":"10.1007/s00294-024-01293-7","DOIUrl":"10.1007/s00294-024-01293-7","url":null,"abstract":"<p><p>The Byr2 kinase of fission yeast Schizosaccharomyces pombe is recruited to the membrane with the assistance of Ras1. Byr2 is also negatively regulated by 14-3-3 proteins encoded by rad24 and rad25. We conducted domain and mutational analysis of Byr2 to determine which region is critical for its binding to 14-3-3 proteins. Rad24 and Rad25 bound to both the Ras interaction domain in the N-terminus and to the C-terminal catalytic domain of Byr2. When amino acid residues S87 and T94 of the Ras-interacting domain of Byr2 were mutated to alanine, Rad24 could no longer bind to Byr2. S402, S566, S650, and S654 mutations in the C-terminal domain of Byr2 also abolished its interaction with Rad24 and Rad25. More than three mutations in the C-terminal domain were required to abolish completely its interaction with 14-3-3 protein, suggesting that multiple residues are involved in this interaction. Expression of the N-terminal domain of Byr2 in wild-type cells lowered the mating ratio, because it likely blocked the interaction of Byr2 with Ste4 and Ras1, whereas expression of the catalytic domain of Byr2 increased the mating ratio as a result of freeing from intramolecular regulation by the N-terminal domain of Byr2. The S87A and T94A mutations of Byr2 increased the mating ratio and attenuated inhibition of Byr2 by Rad24; therefore, these two amino acids are critical for its regulation by Rad24. S566 of Byr2 is critical for activity of Byr2 but not for its interaction with 14-3-3 proteins. In this study, we show that 14-3-3 proteins interact with two separate domains in Byr2 as negative regulators.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}