A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria
Authors: Andrew McMinn
Chun-Yang Li
Lei Wang
Xi-Ying Zhang
Hui-Lin Zhao
Xiu-Lan Chen
Yu-Zhong Zhang
Yin Chen
Yang Yu
Haitao Ding
Jie Yang
Peng Wang
Min Wang
Ian Lidbury
Hai-Nan Su
Bai-Lu Tang
Shuai Zhong
Journal: Nature Communications (2020)
Discipline: Multidisciplinary
Keywords: Predator-prey interactions; marine organic matter cycling; Gram-negative bacterium; Pseudoalteromonas sp. strain CF6-2; metalloprotease pseudoalterin
Affiliations: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China., College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China., Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China., School of Life Sciences, University of Warwick, Coventry, UK., SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China., Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia., State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. ., College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. ., Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China. .

Abstract:  Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean. 

Retracted: No

PubPeer comments:
 There seem to be many discrepancies between the blots shown in the main figures and the  original ones provided in the source data file. For example: For Fig. 2a, a different blot is provided as source data (and the one provided in the main figure seems oddly manipulated as the grey background is  perfect ). In Fig. 4g-h, the blots in the source data look different in terms of relative band intensities. In Fig. 5a (Pseudoalterin with chitin), 4+4 lanes are shown in the main figure, 10 lanes are marked in the source data, and only 9 lanes are annotated in the source data. In Fig. 6i, H79A looks totally different in the source data (just one example of many in Fig. 6). Also, it is quite surprising that none of the blots have any size markers, as this is a Nature Communications policy. , 
 Sorry, we just notice your comment thanks to a recent reminder of the Marine Drugs office. The discrepancies between the blots shown in the main figures and the original ones provided in the source data file are caused by figure stretching, flattening, and or noise,u00a0brightness,u00a0andu00a0contrastu00a0adjustmentu00a0to fit the figure size requirement and to show the results more clearly. All of the handlings did not affect the conclusions of the work. For Fig. 2a, the blot provided in the source data is the same one in the main figure. To clearly show the result and to fit the figure size requirement, elongation, and noise, brightness, and contrast adjustment on the figure were made. For Fig. 4g, the blots in the source data and the main figure look different due to brightness and contrasts adjustment on the figure. For Fig. 4h, we indeed supplied a wrong original figure. The one in the main figure is that exposure for 50 s and the one in the source data is that exposure for 15 s. Please see the original figure exposure for 50 s in Fig. 1c below. For Fig. 5a, we think 4+4 lanes are enough to support our conclusion, thus, only 4+4 lanes are shown in the main text. In the source data, we supplied the original figure of the PAGEu00a0gels. 10 lanes are all annotated in the source data. Indeed, the original figure is not accurately marked as 4+4, we should use two red boxes to mark the lanes as 4+4 accurately consistent with the main figure. A picture with such an accurate mark is shown in Fig. 2b below. For Fig. 6, to fit the figure size requirement, figure stretching, flattening, and or brightness and contrast adjustment were made, leading to the discrepancies between the ones in the source data and those in the main figure. As for the question of the markers, because of space constraints, all of the size markers are supplied in the source data. ![file] , 
 #1 Sorry, we just notice your comment due to a reminder of the Marine Drugs office. The discrepancies between the blots shown in the main figures and the original ones provided in the source data file are caused by figure stretching, flattening, and or noise,u00a0brightness,u00a0andu00a0contrastu00a0adjustmentu00a0to fit the figure size requirement and to show the results more clearly. All of the handlings did not affect the conclusions of the work. For Fig. 2a, the blot provided in the source data is the same one in the main figure. To clearly show the result and to fit the figure size requirement, elongation, and noise, brightness, and contrast adjustment on the figure were made. For Fig. 4g, the blots in the source data and the main figure look different due to brightness and contrasts adjustment on the figure. For Fig. 4h, we indeed supplied a wrong original figure. The one in the main figure is that exposure for 50 s and the one in the source data is that exposure for 15 s. Please see the original figure exposure for 50 s in Fig. 1c below. For Fig. 5a, we think 4+4 lanes are enough to support our conclusion, thus, only 4+4 lanes are shown in the main text. In the source data, we supplied the original figure of the PAGEu00a0gels. 10 lanes are all annotated in the source data. Indeed, the original figure is not accurately marked as 4+4, we should use two red boxes to mark the lanes as 4+4 accurately consistent with the main figure. A picture with such an accurate mark is shown in Fig. 2b below. For Fig. 6, to fit the figure size requirement, figure stretching, flattening, and or brightness and contrast adjustment were made, leading to the discrepancies between the ones in the source data and those in the main figure. As for the question of the markers, because of space constraints, all of the size markers are supplied in the source data. ![file] ,