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Brown JA, Feye KM, Ricke SC. Illumina MiSeq 16S rRNA Gene Library Preparation for Poultry Processing Microbiome Analyses. Methods Mol Biol 2025; 2852:273-288. [PMID: 39235750 DOI: 10.1007/978-1-0716-4100-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, *a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety.This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.
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Affiliation(s)
- Jessica A Brown
- Meat Science and Animal Biologics Discovery, Department of Animal & Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristina M Feye
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery, Department of Animal & Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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2
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Lv P, Shang Y, Zhang Y, Wang W, Liu Y, Su D, Wang W, Li C, Ma C, Yang C. Structural basis for the arsenite binding and translocation of Acr3 antiporter with NhaA folding pattern. FASEB J 2022; 36:e22659. [PMID: 36394534 DOI: 10.1096/fj.202201280r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
The arsenical resistance-3 (ACR3) family constitutes the most common pathway that confers high-level resistance to toxic metalloids in various microorganisms and lower plants. Based on the structural model constructed by AlphaFold2, the Acr3 antiporter from Bacillus subtilis (Acr3Bs ) exhibits a typical NhaA structure fold, with two discontinuous helices of transmembrane (TM) segments, TM4 and TM9, interacting with each other and forming an X-shaped structure. As the structural information available for these important arsenite-efflux pumps is limited, we investigated the evolutionary conservation among 300 homolog sequences and identified three conserved motifs in both the discontinuous helices and TM5. Through site-directed mutagenesis, microscale thermophoresis (MST), and fluorescence resonance energy transfer (FRET) analyses, the identified Motif C in TM9 was found to be a critical element for substrate binding, in which N292 and E295 are involved in substrate coordination, while R118 in TM4 and E322 in TM10 is responsible for structural stabilization. In addition, the highly conserved residues on Motif B of TM5 are potentially key factors in the protonation/deprotonation process. These consensus motifs and residues are essential for metalloid compound translocation of Acr3 antiporters, by framing the core domain and the typical X-shaped of NhaA fold.
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Affiliation(s)
- Peiwen Lv
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Yan Shang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Ye Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Wenkai Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Yuanxiang Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Dandan Su
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Wei Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Chunfang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, P.R. China
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Prokaryotic Na+/H+ Exchangers—Transport Mechanism and Essential Residues. Int J Mol Sci 2022; 23:ijms23169156. [PMID: 36012428 PMCID: PMC9408914 DOI: 10.3390/ijms23169156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Na+/H+ exchangers are essential for Na+ and pH homeostasis in all organisms. Human Na+/H+ exchangers are of high medical interest, and insights into their structure and function are aided by the investigation of prokaryotic homologues. Most prokaryotic Na+/H+ exchangers belong to either the Cation/Proton Antiporter (CPA) superfamily, the Ion Transport (IT) superfamily, or the Na+-translocating Mrp transporter superfamily. Several structures have been solved so far for CPA and Mrp members, but none for the IT members. NhaA from E. coli has served as the prototype of Na+/H+ exchangers due to the high amount of structural and functional data available. Recent structures from other CPA exchangers, together with diverse functional information, have allowed elucidation of some common working principles shared by Na+/H+ exchangers from different families, such as the type of residues involved in the substrate binding and even a simple mechanism sufficient to explain the pH regulation in the CPA and IT superfamilies. Here, we review several aspects of prokaryotic Na+/H+ exchanger structure and function, discussing the similarities and differences between different transporters, with a focus on the CPA and IT exchangers. We also discuss the proposed transport mechanisms for Na+/H+ exchangers that explain their highly pH-regulated activity profile.
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Lv P, Li Y, Wang R, Zhang Y, Wang W, Liu Y, Shang Y, Su D, Wang W, Yang C. The pH sensor and ion binding of NhaD Na
+
/H
+
antiporter from IT superfamily. Mol Microbiol 2022; 118:244-257. [DOI: 10.1111/mmi.14965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Peiwen Lv
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yaru Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Ruimin Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Ye Zhang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Wenkai Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yuanxiang Liu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Yan Shang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Dandan Su
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Wei Wang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology Institute of Microbial Technology, Shandong University Qingdao P. R. China
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Wang L, Zou Q, Yan M, Wang Y, Guo S, Zhang R, Song Y, Li X, Chen H, Shao L, Meng L, Jiang J. Polar or Charged Residues Located in Four Highly Conserved Motifs Play a Vital Role in the Function or pH Response of a UPF0118 Family Na +(Li +)/H + Antiporter. Front Microbiol 2020; 11:841. [PMID: 32457721 PMCID: PMC7221264 DOI: 10.3389/fmicb.2020.00841] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/08/2020] [Indexed: 01/15/2023] Open
Abstract
Functionally uncharacterized UPF0118 family has been re-designated as autoinducer-2 exporter (AI-2E) family since one of its members, Escherichia coli YdgG, was identified to function as an AI-2E. However, it's very likely that AI-2E family members may exhibit significantly distinct functions due to low identities between them. Recently, we identified one member of this family designated as UPF0118 to represent a novel class of Na+(Li+)/H+ antiporters. In this study, we presented that UPF0118, together with its homologs, should represent an independent group of AI-2E family, designated as Na+/H+ Antiporter Group. Notably, this group shows five highly conserved motifs designated as Motifs A to E, which are not detected in the majority of AI-2E family members. Functional analysis established that polar or charged residues located in Motif A to D play a vital role in Na+(Li+)/H+ antiport activity or pH response of UPF0118. However, three basic residues located in Motif E are not involved in the function of UPF0118, although the truncation of C terminus resulted in the non-expression of this transporter. Therefore, we propose that E179-R182-K215-Q217-D251-R292-R293-E296-K298-S30 7 located in Motifs A to D can be used for signature functional motifs to recognize whether AI-2E family members function as Na+(Li+)/H+ antiporters. Current findings positively contribute to the knowledge of molecular mechanism of Na+, Li+ transporting and pH response of UPF0118, and the functional prediction of uncharacterized AI-2E family members.
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Affiliation(s)
- Lidan Wang
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Qiao Zou
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Mingxue Yan
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Yuting Wang
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Sijia Guo
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Rui Zhang
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Yang Song
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Xiaofang Li
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Huiwen Chen
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Li Shao
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Lin Meng
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Biological Sciences, Northeast Agricultural University, Harbin, China
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Feye KM, Ricke SC. Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform. Methods Mol Biol 2019; 1918:213-227. [PMID: 30580412 DOI: 10.1007/978-1-4939-9000-9_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.
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Affiliation(s)
- Kristina M Feye
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Steven C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA.
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Abdel-Motaal H, Meng L, Zhang Z, Abdelazez AH, Shao L, Xu T, Meng F, Abozaed S, Zhang R, Jiang J. An Uncharacterized Major Facilitator Superfamily Transporter From Planococcus maritimus Exhibits Dual Functions as a Na +(Li +, K +)/H + Antiporter and a Multidrug Efflux Pump. Front Microbiol 2018; 9:1601. [PMID: 30061877 PMCID: PMC6055358 DOI: 10.3389/fmicb.2018.01601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 02/01/2023] Open
Abstract
Within major facilitator superfamily (MFS), up to 27 unknown major facilitator families and many members of 60 well-characterized families have been functionally unknown as yet, due to their sharing no or significantly low sequence identity with characterized MFS members. Here we present the first report on the characterization of one functionally unknown MFS transporter designated MdrP with the accession version No. ANU18183.1 from the slight halophile Planococcus maritimus DS 17275T. During the screening of Na+/H+ antiporter genes, we found at first that MdrP exhibits Na+(Li+, K+)/H+ antiport activity, and propose that it should represent a novel class of Na+(Li+, K+)/H+ antiporters. However, we speculate that MdrP may possess an additional protein function. The existence of the signature Motif A of drug/H+antiporter (DHA) family members and phylogenetic analysis suggest that MdrP may also function as a drug efflux pump, which was established by minimum inhibitory concentration tests and drug efflux activity assays. Taken together, this novel MFS transporter exhibits dual functions as a Na+(Li+, K+)/H+ antiporter and a multidrug efflux pump, which will be very helpful to not only positively contribute to the function prediction of uncharacterized MFS members especially DHA1 family ones, but also broaden the knowledge of Na+/H+ antiporters.
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Affiliation(s)
- Heba Abdel-Motaal
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China.,Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Lin Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Zhenglai Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Amro H Abdelazez
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Li Shao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Tong Xu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Fankui Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Shaima Abozaed
- Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Rui Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Juquan Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
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