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Simkovsky R, Parnasa R, Wang J, Nagar E, Zecharia E, Suban S, Yegorov Y, Veltman B, Sendersky E, Schwarz R, Golden SS. Transcriptomic and Phenomic Investigations Reveal Elements in Biofilm Repression and Formation in the Cyanobacterium Synechococcus elongatus PCC 7942. Front Microbiol 2022; 13:899150. [PMID: 35814646 PMCID: PMC9260433 DOI: 10.3389/fmicb.2022.899150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). We performed transcriptomics (RNA-Seq) and phenomics (RB-TnSeq) screens that identified four genes involved in biofilm formation and regulation, more than 25 additional candidates that may impact biofilm formation, and revealed the transcriptomic adaptation to the biofilm state. In so doing, we compared the effectiveness of these two approaches for gene discovery.
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Affiliation(s)
- Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jingtong Wang
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Zecharia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Suban
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Boris Veltman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Center for Circadian Biology, University of California, San Diego, San Diego, CA, United States
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2
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Simkovsky R, Parnasa R, Wang J, Nagar E, Zecharia E, Suban S, Yegorov Y, Veltman B, Sendersky E, Schwarz R, Golden SS. Transcriptomic and Phenomic Investigations Reveal Elements in Biofilm Repression and Formation in the Cyanobacterium Synechococcus elongatus PCC 7942. Front Microbiol 2022; 13:899150. [PMID: 35814646 DOI: 10.1101/2022.01.27.477154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 05/20/2023] Open
Abstract
Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). We performed transcriptomics (RNA-Seq) and phenomics (RB-TnSeq) screens that identified four genes involved in biofilm formation and regulation, more than 25 additional candidates that may impact biofilm formation, and revealed the transcriptomic adaptation to the biofilm state. In so doing, we compared the effectiveness of these two approaches for gene discovery.
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Affiliation(s)
- Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jingtong Wang
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Zecharia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Suban
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Boris Veltman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Center for Circadian Biology, University of California, San Diego, San Diego, CA, United States
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3
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Computational prediction of secreted proteins in gram-negative bacteria. Comput Struct Biotechnol J 2021; 19:1806-1828. [PMID: 33897982 PMCID: PMC8047123 DOI: 10.1016/j.csbj.2021.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction.
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Zheng D, Pang G, Liu B, Chen L, Yang J. Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors. Bioinformatics 2020; 36:3693-3702. [PMID: 32251507 DOI: 10.1093/bioinformatics/btaa230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Identification of virulence factors (VFs) is critical to the elucidation of bacterial pathogenesis and prevention of related infectious diseases. Current computational methods for VF prediction focus on binary classification or involve only several class(es) of VFs with sufficient samples. However, thousands of VF classes are present in real-world scenarios, and many of them only have a very limited number of samples available. RESULTS We first construct a large VF dataset, covering 3446 VF classes with 160 495 sequences, and then propose deep convolutional neural network models for VF classification. We show that (i) for common VF classes with sufficient samples, our models can achieve state-of-the-art performance with an overall accuracy of 0.9831 and an F1-score of 0.9803; (ii) for uncommon VF classes with limited samples, our models can learn transferable features from auxiliary data and achieve good performance with accuracy ranging from 0.9277 to 0.9512 and F1-score ranging from 0.9168 to 0.9446 when combined with different predefined features, outperforming traditional classifiers by 1-13% in accuracy and by 1-16% in F1-score. AVAILABILITY AND IMPLEMENTATION All of our datasets are made publicly available at http://www.mgc.ac.cn/VFNet/, and the source code of our models is publicly available at https://github.com/zhengdd0422/VFNet. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dandan Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Guansong Pang
- Australian Institute for Machine Learning, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
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Xin C, Ban X, Gu Z, Li C, Cheng L, Hong Y, Li Z. Non-classical secretion of 1,4-alpha-glucan branching enzymes without signal peptides in Escherichia coli. Int J Biol Macromol 2019; 132:759-765. [DOI: 10.1016/j.ijbiomac.2019.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 11/16/2022]
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6
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Liang Y, Zhang S. Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou’s general PseAAC via Kullback–Leibler divergence. J Theor Biol 2018; 454:22-29. [DOI: 10.1016/j.jtbi.2018.05.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/19/2018] [Accepted: 05/29/2018] [Indexed: 12/14/2022]
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Liang Y, Zhang S, Ding S. Accurate prediction of Gram-negative bacterial secreted protein types by fusing multiple statistical features from PSI-BLAST profile. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:469-481. [PMID: 29688029 DOI: 10.1080/1062936x.2018.1459835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
Gram-negative bacterial secreted proteins play different roles in invaded eukaryotic cells and cause various diseases. Prediction of Gram-negative bacterial secreted protein types is a meaningful and challenging task. In this paper, we develop a multiple statistical features extraction model based on the dipeptide composition (DPC) descriptor and the detrended moving-average auto-cross-correlation analysis (DMACA) descriptor by PSI-BLAST profile. A 610-dimensional feature vector was constructed on the training set, and the feature extraction model was denoted DPC-DMACA-PSSM. A support vector machine was then selected as a classifier, and the bias-free jackknife test method was used for evaluating the accuracy. Our predictor achieves favourable performance for overall accuracy on the test set and also outperforms the other published approaches. The results show that our approach offers a reliable tool for the identification of Gram-negative bacterial secreted protein types.
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Affiliation(s)
- Y Liang
- a School of Science , Xi'an Polytechnic University , Xi'an 710048 , PR China
| | - S Zhang
- b School of Mathematics and Statistics , Xidian University , Xi'an 710071 , PR China
| | - S Ding
- c Department of Sciences , Dalian Nationalities University , Dalian 116600 , PR China
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8
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Lai HY, Chen XX, Chen W, Tang H, Lin H. Sequence-based predictive modeling to identify cancerlectins. Oncotarget 2018; 8:28169-28175. [PMID: 28423655 PMCID: PMC5438640 DOI: 10.18632/oncotarget.15963] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/24/2017] [Indexed: 11/25/2022] Open
Abstract
Lectins are a diverse type of glycoproteins or carbohydrate-binding proteins that have a wide distribution to various species. They can specially identify and exclusively bind to a certain kind of saccharide groups. Cancerlectins are a group of lectins that are closely related to cancer and play a major role in the initiation, survival, growth, metastasis and spread of tumor. Several computational methods have emerged to discriminate cancerlectins from non-cancerlectins, which promote the study on pathogenic mechanisms and clinical treatment of cancer. However, the predictive accuracies of most of these techniques are very limited. In this work, by constructing a benchmark dataset based on the CancerLectinDB database, a new amino acid sequence-based strategy for feature description was developed, and then the binomial distribution was applied to screen the optimal feature set. Ultimately, an SVM-based predictor was performed to distinguish cancerlectins from non-cancerlectins, and achieved an accuracy of 77.48% with AUC of 85.52% in jackknife cross-validation. The results revealed that our prediction model could perform better comparing with published predictive tools.
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Affiliation(s)
- Hong-Yan Lai
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin-Xin Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Tangshan, China
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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9
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Lima S, Oliveira P, Tamagnini P. The secretion signal peptide of the cyanobacterial extracellular protein HesF is located at its C-terminus. FEMS Microbiol Lett 2017; 364:4036450. [PMID: 28859322 DOI: 10.1093/femsle/fnx160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/25/2017] [Indexed: 11/14/2022] Open
Abstract
Cyanobacteria are photosynthetic prokaryotes, capable of sustaining their growth by converting sunlight into chemical energy by fixing CO2 into organic matter. The cyanobacterium Anabaena sp. PCC 7120 is also capable of fixing atmospheric nitrogen, a metabolic process that occurs in specialized cells, the heterocysts. During the process of heterocyst differentiation, drastic morphological changes occur to prepare the future differentiated cell to accommodate the nitrogen fixation metabolism, which is a highly O2-sensitive process. Recently, we identified an unknown extracellular protein (termed HesF) in Anabaena sp. PCC 7120 and found it to be required for the proper deposition of the polysaccharide layers in the heterocyst cell wall. HesF is a non-classical type I secretion system (T1SS)-dependent secreted substrate, and its secretion signal remained elusive. Here, we report that the secretion signal of HesF is located in its C-terminus. We present evidence that a heterologous reporter protein fused with HesF's secretion signal could be successfully expressed in heterocysts and secreted to the extracellular medium, following hesF's native regulation. This represents the first time that the secretion signal of a cyanobacterial T1SS-dependent substrate is identified, and demonstrates the feasibility of using cyanobacteria for selected protein expression and secretion.
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Affiliation(s)
- Steeve Lima
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, 4169-007 Porto, Portugal
| | - Paulo Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Paula Tamagnini
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, 4169-007 Porto, Portugal
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Nagar E, Zilberman S, Sendersky E, Simkovsky R, Shimoni E, Gershtein D, Herzberg M, Golden SS, Schwarz R. Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus. Environ Microbiol 2017; 19:2862-2872. [PMID: 28585390 DOI: 10.1111/1462-2920.13814] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/23/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022]
Abstract
The hair-like cell appendages denoted as type IV pili are crucial for biofilm formation in diverse eubacteria. The protein complex responsible for type IV pilus assembly is homologous with the type II protein secretion complex. In the cyanobacterium Synechococcus elongatus PCC 7942, the gene Synpcc7942_2071 encodes an ATPase homologue of type II/type IV systems. Here, we report that inactivation of Synpcc7942_2071 strongly affected the suite of proteins present in the extracellular milieu (exo-proteome) and eliminated pili observable by electron microscopy. These results support a role for this gene product in protein secretion as well as in pili formation. As we previously reported, inactivation of Synpcc7942_2071 enables biofilm formation and suppresses the planktonic growth of S. elongatus. Thus, pili are dispensable for biofilm development in this cyanobacterium, in contrast to their biofilm-promoting function in type IV pili-producing heterotrophic bacteria. Nevertheless, pili removal is not required for biofilm formation as evident by a piliated mutant of S. elongatus that develops biofilms. We show that adhesion and timing of biofilm development differ between the piliated and non-piliated strains. The study demonstrates key differences in the process of biofilm formation between cyanobacteria and well-studied type IV pili-producing heterotrophic bacteria.
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Affiliation(s)
- Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Shaul Zilberman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eyal Shimoni
- Weizmann Institute of Science, Electron Microscopy Unit, Rehovot, 7610001 Israel
| | - Diana Gershtein
- The Department of Desalination & Water Treatment, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be'er Sheva 84990, Israel
| | - Moshe Herzberg
- The Department of Desalination & Water Treatment, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Be'er Sheva 84990, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002 Israel
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11
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Nguyen TT, Chon TS, Kim J, Seo YS, Heo M. Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species. J Microbiol 2017; 55:568-582. [PMID: 28664514 DOI: 10.1007/s12275-017-7085-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/02/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
Abstract
Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)-based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Tae-Soo Chon
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
| | - Muyoung Heo
- Department of Physics, Pusan National University, Busan, 46241, Republic of Korea.
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12
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Galea CA, Roberts KD, Zhu Y, Thompson PE, Li J, Velkov T. Functional Characterization of the Unique Terminal Thioesterase Domain from Polymyxin Synthetase. Biochemistry 2017; 56:657-668. [PMID: 28071053 DOI: 10.1021/acs.biochem.6b01139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Polymyxins remain one of the few antibiotics available for treating antibiotic resistant bacteria. Here we describe polymyxin B thioesterase which performs the final step in polymyxin B biosynthesis. Isolated thioesterase catalyzed cyclization of an N-acetylcystamine polymyxin B analogue to form polymyxin B. The thioesterase contained a catalytic cysteine unlike most thioesterases which possess a serine. Supporting this, incubation of polymyxin B thioesterase with reducing agents abolished enzymatic activity, while mutation of the catalytic cysteine to serine significantly decreased activity. NMR spectroscopy demonstrated that uncyclized polymyxin B was disordered in solution, unlike other thioesterase substrates which adopt a transient structure similar to their product. Modeling showed the thioesterase substrate-binding cleft was highly negatively charged, suggesting a mechanism for the cyclization of the substrate. These studies provide new insights into the role of polymyxin thioesterase in polymyxin biosynthesis and highlight its potential use for the chemoenzymatic synthesis of polymyxin lipopeptides.
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Affiliation(s)
| | | | - Yan Zhu
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
| | | | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
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13
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Identification of protein secretion systems in bacterial genomes. Sci Rep 2016; 6:23080. [PMID: 26979785 PMCID: PMC4793230 DOI: 10.1038/srep23080] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/24/2016] [Indexed: 01/08/2023] Open
Abstract
Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annotation tools. We built online and standalone computational tools to accurately predict protein secretion systems and related appendages in bacteria with LPS-containing outer membranes. They consist of models describing the systems’ components and genetic organization to be used with MacSyFinder to search for T1SS-T6SS, T9SS, flagella, Type IV pili and Tad pili. We identified ~10,000 candidate systems in bacterial genomes, where T1SS and T5SS were by far the most abundant and widespread. All these data are made available in a public database. The recently described T6SSiii and T9SS were restricted to Bacteroidetes, and T6SSii to Francisella. The T2SS, T3SS, and T4SS were frequently encoded in single-copy in one locus, whereas most T1SS were encoded in two loci. The secretion systems of diderm Firmicutes were similar to those found in other diderms. Novel systems may remain to be discovered, since some clades of environmental bacteria lacked all known protein secretion systems. Our models can be fully customized, which should facilitate the identification of novel systems.
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14
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Ding JY, Shiu JH, Chen WM, Chiang YR, Tang SL. Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. Front Microbiol 2016; 7:251. [PMID: 27014194 PMCID: PMC4781883 DOI: 10.3389/fmicb.2016.00251] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.
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Affiliation(s)
- Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Jia-Ho Shiu
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Wen-Ming Chen
- Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University Kaohsiung, Taiwan
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica Taipei, Taiwan
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15
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Martínez-García PM, Ramos C, Rodríguez-Palenzuela P. T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes. PLoS One 2015; 10:e0119317. [PMID: 25867189 PMCID: PMC4395097 DOI: 10.1371/journal.pone.0119317] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 11/19/2022] Open
Abstract
T346Hunter (Type Three, Four and Six secretion system Hunter) is a web-based tool for the identification and localisation of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) clusters in bacterial genomes. Non-flagellar T3SS (NF-T3SS) and T6SS are complex molecular machines that deliver effector proteins from bacterial cells into the environment or into other eukaryotic or prokaryotic cells, with significant implications for pathogenesis of the strains encoding them. Meanwhile, T4SS is a more functionally diverse system, which is involved in not only effector translocation but also conjugation and DNA uptake/release. Development of control strategies against bacterial-mediated diseases requires genomic identification of the virulence arsenal of pathogenic bacteria, with T3SS, T4SS and T6SS being major determinants in this regard. Therefore, computational methods for systematic identification of these specialised machines are of particular interest. With the aim of facilitating this task, T346Hunter provides a user-friendly web-based tool for the prediction of T3SS, T4SS and T6SS clusters in newly sequenced bacterial genomes. After inspection of the available scientific literature, we constructed a database of hidden Markov model (HMM) protein profiles and sequences representing the various components of T3SS, T4SS and T6SS. T346Hunter performs searches of such a database against user-supplied bacterial sequences and localises enriched regions in any of these three types of secretion systems. Moreover, through the T346Hunter server, users can visualise the predicted clusters obtained for approximately 1700 bacterial chromosomes and plasmids. T346Hunter offers great help to researchers in advancing their understanding of the biological mechanisms in which these sophisticated molecular machines are involved. T346Hunter is freely available at http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter.
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Affiliation(s)
- Pedro Manuel Martínez-García
- Área de Genética, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, E-29071, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, E-29071, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Avenida Complutense 3, Madrid, 28040, Spain
- * E-mail:
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Hahn A, Stevanovic M, Brouwer E, Bublak D, Tripp J, Schorge T, Karas M, Schleiff E. Secretome analysis of Anabaena sp. PCC 7120 and the involvement of the TolC-homologue HgdD in protein secretion. Environ Microbiol 2014; 17:767-80. [PMID: 24890022 DOI: 10.1111/1462-2920.12516] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 05/18/2014] [Indexed: 12/01/2022]
Abstract
Secretion of proteins is a central strategy of bacteria to influence and respond to their environment. Until now, there has been very few discoveries regarding the cyanobacterial secrotome or the secretion machineries involved. For a mutant of the outer membrane channel TolC-homologue HgdD of Anabaena sp. PCC 7120, a filamentous and heterocyst-forming cyanobacterium, an altered secretome profile was reported. To define the role of HgdD in protein secretion, we have developed a method to isolate extracellular proteins of Anabaena sp. PCC 7120 wild type and an hgdD loss-of-function mutant. We identified 51 proteins of which the majority is predicted to have an extracellular secretion signal, while few seem to be localized in the periplasmic space. Eight proteins were exclusively identified in the secretome of wild-type cells, which coincides with the distribution of type I secretion signal. We selected three candidates and generated hemagglutinin-tagged fusion proteins which could be exclusively detected in the extracellular protein fraction. However, these proteins are not secreted in the hgdD-mutant background, where they are rapidly degraded. This confirms a direct function of HgdD in protein secretion and points to the existence of a quality control mechanism at least for proteins secreted in an HgdD-dependent pathway.
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Affiliation(s)
- Alexander Hahn
- Institute of Molecular Biosciences, Cell Biology of Plants, Goethe University, Max-von-Laue Str. 9, Frankfurt/am Main, 60438, Germany
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Bacterial endosymbiosis in a chordate host: long-term co-evolution and conservation of secondary metabolism. PLoS One 2013; 8:e80822. [PMID: 24324632 PMCID: PMC3851785 DOI: 10.1371/journal.pone.0080822] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022] Open
Abstract
Intracellular symbiosis is known to be widespread in insects, but there are few described examples in other types of host. These symbionts carry out useful activities such as synthesizing nutrients and conferring resistance against adverse events such as parasitism. Such symbionts persist through host speciation events, being passed down through vertical transmission. Due to various evolutionary forces, symbionts go through a process of genome reduction, eventually resulting in tiny genomes where only those genes essential to immediate survival and those beneficial to the host remain. In the marine environment, invertebrates such as tunicates are known to harbor complex microbiomes implicated in the production of natural products that are toxic and probably serve a defensive function. Here, we show that the intracellular symbiont Candidatus Endolissoclinum faulkneri is a long-standing symbiont of the tunicate Lissoclinum patella, that has persisted through cryptic speciation of the host. In contrast to the known examples of insect symbionts, which tend to be either relatively recent or ancient relationships, the genome of Ca. E. faulkneri has a very low coding density but very few recognizable pseudogenes. The almost complete degradation of intergenic regions and stable gene inventory of extant strains of Ca. E. faulkneri show that further degradation and deletion is happening very slowly. This is a novel stage of genome reduction and provides insight into how tiny genomes are formed. The ptz pathway, which produces the defensive patellazoles, is shown to date to before the divergence of Ca. E. faulkneri strains, reinforcing its importance in this symbiotic relationship. Lastly, as in insects we show that stable symbionts can be lost, as we describe an L. patella animal where Ca. E. faulkneri is displaced by a likely intracellular pathogen. Our results suggest that intracellular symbionts may be an important source of ecologically significant natural products in animals.
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