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Jordan T. Schouten - One of the best experts on this subject based on the ideXlab platform.
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Whole-genome comparison maps show diversity between Brevibacillus phage clusters.
2016Co-Authors: Jordan A. Berg, Bryan D. Merrill, Justin T. Crockett, Kyle P. Esplin, Marlee R. Evans, Karli E. Heaton, Jared A. Hilton, Jonathan R. Hyde, Morgan S. Mcbride, Jordan T. SchoutenAbstract:A Phamerator [30] whole genome comparison map was prepared using a representative member of each cluster. Boxes on top of the genome ruler indicate genes that are expressed in the forward direction while those below the ruler are expressed in the reverse direction. Gene products are numbered. Colored boxes correspond to encoded proteins that belong to a particular pham (family of homologous proteins) found in any of the ten Brevibacillus phages, while white boxes denote an orpham (an ORF not belonging to a pham). Purple, red, or green lines between genomes illustrate regions of nucleotide similarity. Emery gps 4–5 represents a frameshift event by ribosomal slippage. Functions annotated were compiled from both BLAST and CDD searches. Abbreviations used include: MGEBNA (mannosyl-glycoprotein endo-beta-N-acetylglucosamidase); XRE (XRE family transcriptional regulator); TR (Trascriptional regulator); ssDNA binding (single-stranded DNA binding); DNA rep (DNA replication); RecU (recombinase RecU); SSp DNA meth (Site-specific DNA methylase); RNA pol sigma 24 (RNA polymerase sigma 24); MD hydrolase (Metal-dependent hydrolase); DNA pol III G/T (DNA polymerase III subunit gamma/tau); Regulator of CC (Regulator of chromosome condensation family); NALAAC (N-acetylmuramoyl-L-alanine amidase CwlA); Spo0E (Sporulation protein Spo0E OR Spo0E-like sporulation regulator family); DNA pol III (DNA polymerase III); RNA pol sigma (RNA polymerase sigma factor); FtsK (Cell division protein FtsK); DNA pol I (DNA polymerase I); NALA amidase (N-acetylmuramoyl-L-alanine amidase); XRE (XRE family transcriptional regulator); Gene reg B (Accessory gene regulator B family); DNA-directed DNA pol A (DNA-directed DNA polymerase, family A); RNA pol sigma (RNA polymerase sigma factor); V spor K, ATPase (stage V sporulation protein K, ATPase AAA); Ac-di syn (cobyrinic acid ac-diamide synthase); XerD (site specific recombinase XerD); Reg s, luxR (bacterial regulatory s, luxR family); BN DNA binding (Bacterial nucleoid DNA-binding); Exc ABC (Excinuclease ABC); CJE RusA (Crossover Junction Endodeoxyribonuclease RusA); Asp-tRNA amidotrans B (Aspartyl-tRNA amidotransferase subunit B); ssDNA-sp exonuclease (Single-stranded DNA-specific exonuclease).
Pereira, Leandro De Mattos - One of the best experts on this subject based on the ideXlab platform.
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O papel biológico das enzimas iso-funcionais não homólogas em linhagens de Escherichia coli
2014Co-Authors: Pereira, Leandro De MattosAbstract:Made available in DSpace on 2018-11-27T10:24:22Z (GMT). No. of bitstreams: 2 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) leandro_pereira_ioc_dout_2014.pdf: 3176805 bytes, checksum: 6d28d35d7bdc81fddb0e501599b191e2 (MD5) Previous issue date: 2014Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil.Enzimas são proteínas que catalisam reações bioquímicas, funcionando como catalisadores biológicos naturais. Cada enzima tem um nome recomendado e número atribuído por uma comissão especializada, a "Enzyme Comission", um número que classifica a enzima de acordo com a reação que catalisa e de acordo com a sua função enzimática. As enzimas que catalisam a mesma reação geralmente têm uma alta semelhança entre as suas estruturas primária (por Ex. homólogos), isto reflete na semelhança das estruturas terciárias, o que sugere uma origem evolutiva comum. Contudo, agumas enzimas são capazes de catalizar a mesma transformação química e possuem distintas estruturas terciárias, são originadas de eventos evolutivos independentes, por processos de convergência funcional. Estas enzimas são conhecidas como enzimas isofuncionais não homólogas isofuncionais (NISEs). Analisando dados genômicos de diferentes linhagens de Escherichia coli, observamos a presença simultânea de NISEs no mesmo genoma. Não sabemos o significado biológico ou o impacto sobre o metabolismo da presença destas enzimas no mesmo genoma Neste trabalho nós mostramos que estas enzimas têm diferentes estruturas terciárias confirmados pela validação estrutural e várias outras características funcionais diferentes, por exemplo, afinidade diferente para um substrato, diferentes padrões cinéticos e co-fatores, diferenças na estabilidade e regulação. Estas enzimas também podem ter diferentes padrões de expressão gênica e co-expressão e regulação, diferentes parceiros nas redes de interações proteína-proteína. A análise do número de cópias mostrou um aumento do número de cópias (Ex. amplificação gênica) de enzimas do metabolismo central envolvidas em processos essenciais, tais como: recombinação genética: (RusA: Crossover Junction Endodeoxyribonuclease RusA, EC 3.1.22.4), a modificação da parede celular e morte celular programada (RrrD: Lysozyme RrrD, EC 3.2.1.17), a subversão da resposta imune (UshA, 5'-nucleotidase, EC 3.1.3.5), formação de biofilmes, células de persistência (PlsB: Glycerol-3-phosphate acyltransferase, EC 2.3.1.15). Os resultados mostram que NISEs em em linhagens de E. coli não representam casos de redundância funcional, tais enzimas aumentam a adaptação e flexibilidade metabôlica da bactéria para lidar com diferentes desafios ambientais.Enzymes are proteins that catalyze biochemical reactions, functioning as natural biological catalysts. Each enzyme has a recommended name and number assigned by a specialized committee, the "Enzyme Comission", a number that ranks the enzyme according to the reaction that it catalyzes and according to its enzymatic function. The enzymes that catalyze the same reaction usually have a high similarity between their primary structures (by Ex. homologous) this similarity is reflected in tertiary structures, suggesting a common evolutionary origin. However, some enzymes are able to catalyze the same chemical transformational and have distinct tertiary structure, are originated from distints events evolutives by process of functional convergence. Such enzymes are known as non-homologous enzymes isofuncionais (NISEs) or similar enzymes. Analyzing genomic data of different strains of Escherichia coli, we observed the simultaneous presence of NISEs the same genome. Do not know the biological significance or the impact on the metabolism of the presence of these enzymes in the same genome In this work we have shown that these enzymes have different tertiary structures confirmed by structural validation, and have several other different functional features, for example: different affinity for a substrate, different kinetic patterns and co-factors, different stability and regulation. We also observed that these enzymes may have different expression patterns and gene co-expression and regulation, different partners in the networks of protein-protein interactions. The analysis of the number of copies showed an increased number (Ex. gene amplification) of copies of some structural forms with analogy cases of central metabolism, enzymes involved in essential processes such as: genetic recombination: (RusA: Crossover Junction endodeoxiribonuclease, EC 3.1.22.4), modification of cell wall and programmed cell death (RrrD: lysozyme), subversion of the immune response (Usha, 5'-nucleotidase, EC 3.1.3.5) formation biofilms and cell persistence (PlsB: acetyl gligerol 3-phosphatase, EC 2.3.1.15). The results show that NISES don\2019t represent cases of functional redundancy; such enzymes increase metabolic flexibility of bacteria to handle different environmental challenges
Jordan A. Berg - One of the best experts on this subject based on the ideXlab platform.
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Whole-genome comparison maps show diversity between Brevibacillus phage clusters.
2016Co-Authors: Jordan A. Berg, Bryan D. Merrill, Justin T. Crockett, Kyle P. Esplin, Marlee R. Evans, Karli E. Heaton, Jared A. Hilton, Jonathan R. Hyde, Morgan S. Mcbride, Jordan T. SchoutenAbstract:A Phamerator [30] whole genome comparison map was prepared using a representative member of each cluster. Boxes on top of the genome ruler indicate genes that are expressed in the forward direction while those below the ruler are expressed in the reverse direction. Gene products are numbered. Colored boxes correspond to encoded proteins that belong to a particular pham (family of homologous proteins) found in any of the ten Brevibacillus phages, while white boxes denote an orpham (an ORF not belonging to a pham). Purple, red, or green lines between genomes illustrate regions of nucleotide similarity. Emery gps 4–5 represents a frameshift event by ribosomal slippage. Functions annotated were compiled from both BLAST and CDD searches. Abbreviations used include: MGEBNA (mannosyl-glycoprotein endo-beta-N-acetylglucosamidase); XRE (XRE family transcriptional regulator); TR (Trascriptional regulator); ssDNA binding (single-stranded DNA binding); DNA rep (DNA replication); RecU (recombinase RecU); SSp DNA meth (Site-specific DNA methylase); RNA pol sigma 24 (RNA polymerase sigma 24); MD hydrolase (Metal-dependent hydrolase); DNA pol III G/T (DNA polymerase III subunit gamma/tau); Regulator of CC (Regulator of chromosome condensation family); NALAAC (N-acetylmuramoyl-L-alanine amidase CwlA); Spo0E (Sporulation protein Spo0E OR Spo0E-like sporulation regulator family); DNA pol III (DNA polymerase III); RNA pol sigma (RNA polymerase sigma factor); FtsK (Cell division protein FtsK); DNA pol I (DNA polymerase I); NALA amidase (N-acetylmuramoyl-L-alanine amidase); XRE (XRE family transcriptional regulator); Gene reg B (Accessory gene regulator B family); DNA-directed DNA pol A (DNA-directed DNA polymerase, family A); RNA pol sigma (RNA polymerase sigma factor); V spor K, ATPase (stage V sporulation protein K, ATPase AAA); Ac-di syn (cobyrinic acid ac-diamide synthase); XerD (site specific recombinase XerD); Reg s, luxR (bacterial regulatory s, luxR family); BN DNA binding (Bacterial nucleoid DNA-binding); Exc ABC (Excinuclease ABC); CJE RusA (Crossover Junction Endodeoxyribonuclease RusA); Asp-tRNA amidotrans B (Aspartyl-tRNA amidotransferase subunit B); ssDNA-sp exonuclease (Single-stranded DNA-specific exonuclease).
Bryan D. Merrill - One of the best experts on this subject based on the ideXlab platform.
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Whole-genome comparison maps show diversity between Brevibacillus phage clusters.
2016Co-Authors: Jordan A. Berg, Bryan D. Merrill, Justin T. Crockett, Kyle P. Esplin, Marlee R. Evans, Karli E. Heaton, Jared A. Hilton, Jonathan R. Hyde, Morgan S. Mcbride, Jordan T. SchoutenAbstract:A Phamerator [30] whole genome comparison map was prepared using a representative member of each cluster. Boxes on top of the genome ruler indicate genes that are expressed in the forward direction while those below the ruler are expressed in the reverse direction. Gene products are numbered. Colored boxes correspond to encoded proteins that belong to a particular pham (family of homologous proteins) found in any of the ten Brevibacillus phages, while white boxes denote an orpham (an ORF not belonging to a pham). Purple, red, or green lines between genomes illustrate regions of nucleotide similarity. Emery gps 4–5 represents a frameshift event by ribosomal slippage. Functions annotated were compiled from both BLAST and CDD searches. Abbreviations used include: MGEBNA (mannosyl-glycoprotein endo-beta-N-acetylglucosamidase); XRE (XRE family transcriptional regulator); TR (Trascriptional regulator); ssDNA binding (single-stranded DNA binding); DNA rep (DNA replication); RecU (recombinase RecU); SSp DNA meth (Site-specific DNA methylase); RNA pol sigma 24 (RNA polymerase sigma 24); MD hydrolase (Metal-dependent hydrolase); DNA pol III G/T (DNA polymerase III subunit gamma/tau); Regulator of CC (Regulator of chromosome condensation family); NALAAC (N-acetylmuramoyl-L-alanine amidase CwlA); Spo0E (Sporulation protein Spo0E OR Spo0E-like sporulation regulator family); DNA pol III (DNA polymerase III); RNA pol sigma (RNA polymerase sigma factor); FtsK (Cell division protein FtsK); DNA pol I (DNA polymerase I); NALA amidase (N-acetylmuramoyl-L-alanine amidase); XRE (XRE family transcriptional regulator); Gene reg B (Accessory gene regulator B family); DNA-directed DNA pol A (DNA-directed DNA polymerase, family A); RNA pol sigma (RNA polymerase sigma factor); V spor K, ATPase (stage V sporulation protein K, ATPase AAA); Ac-di syn (cobyrinic acid ac-diamide synthase); XerD (site specific recombinase XerD); Reg s, luxR (bacterial regulatory s, luxR family); BN DNA binding (Bacterial nucleoid DNA-binding); Exc ABC (Excinuclease ABC); CJE RusA (Crossover Junction Endodeoxyribonuclease RusA); Asp-tRNA amidotrans B (Aspartyl-tRNA amidotransferase subunit B); ssDNA-sp exonuclease (Single-stranded DNA-specific exonuclease).
Justin T. Crockett - One of the best experts on this subject based on the ideXlab platform.
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Whole-genome comparison maps show diversity between Brevibacillus phage clusters.
2016Co-Authors: Jordan A. Berg, Bryan D. Merrill, Justin T. Crockett, Kyle P. Esplin, Marlee R. Evans, Karli E. Heaton, Jared A. Hilton, Jonathan R. Hyde, Morgan S. Mcbride, Jordan T. SchoutenAbstract:A Phamerator [30] whole genome comparison map was prepared using a representative member of each cluster. Boxes on top of the genome ruler indicate genes that are expressed in the forward direction while those below the ruler are expressed in the reverse direction. Gene products are numbered. Colored boxes correspond to encoded proteins that belong to a particular pham (family of homologous proteins) found in any of the ten Brevibacillus phages, while white boxes denote an orpham (an ORF not belonging to a pham). Purple, red, or green lines between genomes illustrate regions of nucleotide similarity. Emery gps 4–5 represents a frameshift event by ribosomal slippage. Functions annotated were compiled from both BLAST and CDD searches. Abbreviations used include: MGEBNA (mannosyl-glycoprotein endo-beta-N-acetylglucosamidase); XRE (XRE family transcriptional regulator); TR (Trascriptional regulator); ssDNA binding (single-stranded DNA binding); DNA rep (DNA replication); RecU (recombinase RecU); SSp DNA meth (Site-specific DNA methylase); RNA pol sigma 24 (RNA polymerase sigma 24); MD hydrolase (Metal-dependent hydrolase); DNA pol III G/T (DNA polymerase III subunit gamma/tau); Regulator of CC (Regulator of chromosome condensation family); NALAAC (N-acetylmuramoyl-L-alanine amidase CwlA); Spo0E (Sporulation protein Spo0E OR Spo0E-like sporulation regulator family); DNA pol III (DNA polymerase III); RNA pol sigma (RNA polymerase sigma factor); FtsK (Cell division protein FtsK); DNA pol I (DNA polymerase I); NALA amidase (N-acetylmuramoyl-L-alanine amidase); XRE (XRE family transcriptional regulator); Gene reg B (Accessory gene regulator B family); DNA-directed DNA pol A (DNA-directed DNA polymerase, family A); RNA pol sigma (RNA polymerase sigma factor); V spor K, ATPase (stage V sporulation protein K, ATPase AAA); Ac-di syn (cobyrinic acid ac-diamide synthase); XerD (site specific recombinase XerD); Reg s, luxR (bacterial regulatory s, luxR family); BN DNA binding (Bacterial nucleoid DNA-binding); Exc ABC (Excinuclease ABC); CJE RusA (Crossover Junction Endodeoxyribonuclease RusA); Asp-tRNA amidotrans B (Aspartyl-tRNA amidotransferase subunit B); ssDNA-sp exonuclease (Single-stranded DNA-specific exonuclease).