Brambila-Tapia Aniel Jessica Leticia, Perez-Rueda Ernesto, Barrios Humberto, Dávalos-Rodríguez Nory Omayra, Dávalos-Rodríguez Ingrid Patricia, Cardona-Muñoz Ernesto Germán, Salazar-Páramo Mario
Departamento de Psicología Básica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Sierra Mojada #950, colonia Independencia, C.P. 44340, Guadalajara, Jalisco, Mexico.
Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas (IIMAS), Unidad Académica de Ciencias y Tecnología Universidad Nacional Autónoma de México (UNAM), Mérida, Yucatán, Mexico.
Curr Microbiol. 2017 Aug;74(8):915-920. doi: 10.1007/s00284-017-1265-3. Epub 2017 May 16.
A systematic analysis of beta-lactamases based on comparative proteomics has not been performed thus far. In this report, we searched for the presence of beta-lactam-related proteins in 591 bacterial proteomes belonging to 52 species that are pathogenic to humans. The amino acid sequences for 19 different types of beta-lactamases (ACT, CARB, CifA, CMY, CTX, FOX, GES, GOB, IMP, IND, KPC, LEN, OKP, OXA, OXY, SHV, TEM, NDM, and VIM) were obtained from the ARG-ANNOT database and were used to construct 19 HMM profiles, which were used to identify potential beta-lactamases in the completely sequenced bacterial proteomes. A total of 2877 matches that included the word "beta-lactamase" and/or "penicillin" in the functional annotation and/or in any of its regions were obtained. These enzymes were mainly described as "penicillin-binding proteins," "beta-lactamases," and "metallo-beta-lactamases" and were observed in 47 of the 52 species studied. In addition, proteins classified as "beta-lactamases" were observed in 39 of the species included. A positive correlation between the number of beta-lactam-related proteins per species and the proteome size was observed (R 0.78, P < 0.00001). This correlation partially explains the high presence of beta-lactam-related proteins in large proteomes, such as Nocardia brasiliensis, Bacillus anthracis, and Mycobacterium tuberculosis, along with their absence in small proteomes, such as Chlamydia spp. and Mycoplasma spp. We detected only five types of beta-lactamases (TEM, SHV, CTX, IMP, and OXA) and other related proteins in particular species that corresponded with those reported in the literature. We additionally detected other potential species-specific beta-lactamases that have not yet been reported. In the future, better results will be achieved due to more accurate sequence annotations and a greater number of sequenced genomes.
迄今为止，尚未基于比较蛋白质组学对β-内酰胺酶进行系统分析。在本报告中，我们在属于52种对人类致病的细菌蛋白质组中搜索了β-内酰胺相关蛋白的存在情况。从ARG-ANNOT数据库中获取了19种不同类型β-内酰胺酶（ACT、CARB、CifA、CMY、CTX、FOX、GES、GOB、IMP、IND、KPC、LEN、OKP、OXA、OXY、SHV、TEM、NDM和VIM）的氨基酸序列，并用于构建19个隐马尔可夫模型（HMM）图谱，这些图谱用于在完全测序的细菌蛋白质组中鉴定潜在的β-内酰胺酶。在功能注释和/或其任何区域中，总共获得了2877个包含“β-内酰胺酶”和/或“青霉素”一词的匹配项。这些酶主要被描述为“青霉素结合蛋白”、“β-内酰胺酶”和“金属β-内酰胺酶”，在所研究的52个物种中的47个物种中观察到。此外，在所纳入的39个物种中观察到了归类为“β-内酰胺酶”的蛋白质。观察到每个物种中β-内酰胺相关蛋白的数量与蛋白质组大小之间存在正相关（R = 0.78，P < 0.00001）。这种相关性部分解释了在大型蛋白质组（如巴西诺卡菌、炭疽芽孢杆菌和结核分枝杆菌）中β-内酰胺相关蛋白的高丰度，以及在小型蛋白质组（如衣原体属和支原体属）中它们的缺失。我们在特定物种中仅检测到五种类型的β-内酰胺酶（TEM、SHV、CTX、IMP和OXA）以及其他相关蛋白，这些与文献报道的一致。我们还检测到了其他尚未报道的潜在物种特异性β-内酰胺酶。未来，由于更准确的序列注释和更多已测序的基因组，将会取得更好的结果。
